MolNFT v1 · #78223 · protein

Crystal structure of dipeptidase from streptomyces coelicolor complexed with phosphinate pseudodipeptide L-phe-D-asp

3S2M: “Crystal structure of dipeptidase from streptomyces coelicolor complexed with phosphinate pseudodipeptide…”. X-ray diffraction, 2 ligands (P5D, ZN), 2 pockets (best druggability 0.62). MolNFT v1 #78223 on GenesisL1: 3D structure…

PDB: 3S2M
Type: protein
Length: 393 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidase
UniProt: Q93J45
Ligands: P5D, ZN
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptidase	protein	393	51% helix, 12% strand	Q93J45

Ligands and binding sites

P5D · (2R)-2-{[(S)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]methyl}butanedioic acid · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 6 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	455	0.62	0.76	49	P5D, ZN
2	110	0.44	0.78	20	empty

Compared structures

3S2M · Crystal structure of dipeptidase from Streptomyces coelicolor complexed with phosphinate… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q93J45
Elsewhere: RCSB PDB 3S2M · PDBe 3S2M · UniProt Q93J45

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